Paolo
The surge is most likely a lean/airleak issue. As Cal mentioned, you want to have a proper bench sync to start. Just get the slides as low as you can, a tiny gap is fine. You want to get the most operation out of your idle knob as possible; the largest range you can.
Let's try a few things. I know it may seem unlikely but while the bike is idling push and pull the carb rack up and down and see if it changes the idle. If it does then try and tighten up the carb to intake manifold insulator clamps more. Those need to be tighter than you think.
Try putting some tape around your intake filter to restrict some flow, see if things improve on the surging.
I'm sure you posted it before but what jetting are you running?
You have sooty plugs but lean running symptoms. There are many circuits running in the mixture system. You could be lean in one area and rich in another. I will give you some assurance on the sooty plugs though, I have my 550 tuned as best as It's ever been. No popping, sputtering, hesitation, it's a linear and smooth power delivery. I richened up the pilot circuit to achieve this and my plugs will look sooty very quickly if I leave it idling or just put around. When I go for a spirited ride and get to that self cleaning heat range, the plugs turn golden brown. In my opinion, it's the nature of these bikes. Better a bit rich than lean.
Do you have any sets of clean plugs? pop them in and let it idle for a few minutes with a fan, pull them and take a look. Give us an idea if you have a lean pilot circuit.
Report back when you can.
